scribenick bobP

<mscottm> thanks bobP!

<joanne> hello!

<joanne> What's "Idler's" mean (on the right hand side of mibbit)

<michel> elgar presented TMO at bio-it world

Michel: Discussion of paper, more detail about use case
... Adrian Coulet w. sopharm; We are lucky to have Adrian participate

<adriencoulet> thank you !

Michel: 1) warfarin 2) breast cancer; 2) let's talk about this story

Scott: Talked w Daniel Rueben(?) and John Madden about bc

<adriencoulet> Daniel Rubin

<adriencoulet> ?

Scott: lots of people understand the terminology involved
... consider oncoDX and Mammaprint(?)
... making use of molecular info about patient in order to stratify, to make better choices
... also discover clinical trials and drugs in development
... easily understandable to the audience; reduces costs and needless suffering

<michel> OncoDX: http://www.oncotypedx.com/en-US/Breast/HealthcareProfessional/ClinicalSummary.aspx

Scott: increases patient care. All nice goals for theoretical use cases

<michel> Mammaprint: http://www.agendia.com/pages/mammaprint/21.php

Scott: note that each use case applied to millions of women
... also clinician-single patient application. Still needs to be implemented in hospital IT

<michel> paper: https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

Scott: I wrote a few things in
... not sitting on bc data, but we do have some kidney transplant data.
... might be able to get some data from Mammaprint people

Joanne: Data are critical; any public bc datasets?
... can bring in IO too

Scott - breaking up!

Scott: ... data did not have info, embedded in a giant object model

<scribe> ... dropped effort b/c did not want to parse thru it all.

UNKNOWN_SPEAKER: working w theoretical scenarios, hardest challenge is to come up w realistic gx profile
... nobody reading article will need to look at differential expression
... we are putting forth a proof-of-concept
... but, true, the more realistic the better

<adriencoulet> http://www.pharmgkb.org/do/serve?objId=PA443560&objCls=Disease#tabview=tab6

<adriencoulet> some PGx about breast neoplasms

Joanne: Knows group w/in Zach's dept
... Ponolacco(?)

Michel: Adrian has posted this link w. data

<joanne> thanks Adrien!

We lost Adrian

<joanne> Peter Tonellato <Peter_Tonellato at hms.harvard.edu>

Michel: Shows down to alleles
... mostly tamoxifen datasets

<mscottm> All: when you aren't speaking, please mute (it should help us to get rid of the echo)

<joanne> Web Site for Peter Tonellato's group: http://lpm.hms.harvard.edu/

Michel: #7 looks good! Joanne agrees

<michel> http://www.pharmgkb.org/do/serve?objId=PA646603&objCls=PhenotypeDataset#tabview=tab2

Males do get bc.

Michel: Cool w. alleles, but no outcomes here. Need to read the paper to understand remission
... convert to RDF, then query?
... these are the actual data; Not been formalized to RDF yet.
... will require some significant curation. Columnn headers require some work.
... base change definitions, we will have to parse this on a case-by-case basis

Matthias: commenting here

Joanne will develop use cases

Michel: Need to download the data and parse

<matthias_samwald> e.g., http://www.snpedia.com/index.php/CYP3A5 lists the allele names (*1, *5 etc.), but unfortunately not in a way that would make it show up in the current RDF version of SNPedia.

Joanne: TMO or separate ontology?

Matthias: Started ont, tried to align everything w TMO and other authorities
... raw at the moment. Want to use it for clinical decision support

Scott: Do you have use cases? Interviewing clinician?

Matthias: Blue sky research at the moment.

<mscottm> Univ. of Nancy

Adrian: PhD pharmacogenomics text mining

<mscottm> Adrien: Prof at Univ of Nancy, did PhD with PharmGKB, from Mark Musen's lab (just returned from NCBO to France)

<mscottm> Adrien recently published work on SO-Pharm

Michel: Submit 1st week in May(?)

<adriencoulet> http://www.loria.fr/~coulet/

Michel: important to develop use case, as it relates to PharmGKB website

Scott: Maybe hook up w Terminology call

<michel> https://docs.google.com/drawings/edit?id=1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI&hl=en&authkey=CIT4rcwM

Michel: Look at diagram, a general model in advance of use case
... ontology would be purple boxes

Matthias asking about gene variant as attribute of population and not of person

Scott: Better to have sample population associated w gene frequency

<joanne> i have to leave now. Would someone volunteer to contact me later and be willing to go over the diagram with me - preferably tomorrow? Michel, ideally, but if you can't someone else who understands it as well (not having generated)

Scott: (Scott was asking here...)

<joanne> bye.

Matthias: Arrow from freq to pop?

<adriencoulet> bye :)

Michel: Gene variant is still part of an individual
... to assoc freq, has to be a sub-type
... variant in population is a sub-class of variant in individual(?), has more property restriction

Matthias: In my view, it's not really a subclass

Scott: One class of snp, diff freqs of measurement in different population

Michel: But we do assign(?) these genes to specific individuals

Scott: We could have a number of models; test would be how to find w owl or sparql
... demonstate the differences of how the different models work
... brca1 has certain freq in pop, but fewer known alleles which are known to be associated w cancer
... compared to snps which are known to be associated w cancer
... gwas might have millions of snps to go thru for genome
... brca measure is more like a read-out of a prognosis.
... Carry out further w. email exchange.

Michel: Add this discussion to the paper

<mscottm> Scott was actually saying that the BRCA1 allele is directly associated with a type of cancer.

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Regrets: Elgar Trish

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Got date from IRC log name: 14 Apr 2011
Guessing minutes URL: http://www.w3.org/2011/04/14-hcls2-minutes.html
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